TFM2_16S_amplicons_analysis
lrubinat
5/30/2017
1) 16S amplicons
1.1) Data overview
The dataset “Taraspina 16S miTags” contains reads from 122 samples of Malaspina. On average, each sample contains 45940 reads:
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 405 20410 33100 45940 68340 148200
Overall reads per sample:
1.2) Normalization
In order to keep as many samples as possible, we rarefy at 16509 reads per sample. By that, we loose 31 samples, and after removing the exluded samples in the 16S dataset (to make them comparable), we end up with a normalized dataset containing 91 samples and 8173 OTUs.
Datasets summary:
dim(tb16_tax) #original dataset## [1] 9114 128dim(tb16_tax_occur) #original dataset with occurrence data alone## [1] 9114 122dim(tb16_tax_occur_min16509) #dataset without samples with less than 16509 OTUs## [1] 8881 91dim(tb16_tax_occur_ss16509_no_cero) #rarefied dataset## [1] 91 81731.3) General community analysis
1.3.1) Richness and evenness (Shannon index)
Most of the samples take Shannon Index values around 4:
1.3.2) Richness: OTU number
Lowest number of OTUs per sample:
## [1] 618Maximum number of OTUs per sample:
## [1] 1660In most of the samples, we can identify about 1400 OTUs:
1.3.3) Index of evenness
1.3.3.1) Pielou’s index
The Pielou index (constrained between 0 and 1) takes values closer to 1 as the variation of species proportion in a sample increases. Our samples get values around 0.6, meaning that the numerical composition of different OTUs in a sample is not so variable - we might observe certain dominant species.
1.3.4) Abundance Models
Most of the OTUs show very few occurrences, suggesting that we will probably be able to identify a significant ammount of rare otus:
1.3.4.1) Rank-Abundance or Dominance/Diversity Model (“radfit”)
The OTUs abundance distribution fits relativelly close to log-normal model.
1.3.4.2) Preston’s Lognormal Model
According to Preston’s lognormal model fit into species frequencies groups, we’re missing ~262 species:
veiledspec(tb16_tax_occur_ss16509_prestonfit)## Extrapolated Observed Veiled
## 9143.6079 8881.0000 262.6079
When computing Prestons’ lognormal model fit without pooling data into groups, we miss ~251 species:
## Extrapolated Observed Veiled
## 9132.6917 8881.0000 251.69171.3.5) Rarefaction curves of rarefied and non-rarefied datasets
1.3.6) Beta diversity
1.3.6.1) Dissimilarity matrix using Bray-Curtis index:
The Bray-Curtis dissimilarity, constrained between 0 (minimum distance) and 1 (highest dissimilarity) allows us to quantify the differences between samples according to the composition and relative abundance of their OTUs. In our dataset, most of the samples pairs take dissimilarity values between between 2 and 4, meaning that their composition is substantially similar.
1.3.6.2) Hierarchical clustering
The stations seem to form clusters according to geographic localization, but there are no evident clusters separated from the general groups.
(To be done: assign Longhurst provinces information to each station and check if any of the central clusters is meaningful regarding to the samples’ geographical location)
1.3.6.3) Non-metric multidimensional scaling
We can identify a prominent group in the central part of the NMDS plot and a few outliers in the central-high edge of the plot. The stress parameter takes a value below 0.2, suggesting that the plot is acceptable.
##
## Call:
## monoMDS(dist = tb16_tax_occur_ss16509_no_cero.bray)
##
## Non-metric Multidimensional Scaling
##
## 91 points, dissimilarity 'bray', call 'vegdist(x = tb16_tax_occur_ss16509_no_cero, method = "bray")'
##
## Dimensions: 2
## Stress: 0.1477793
## Stress type 1, weak ties
## Scores scaled to unit root mean square, rotated to principal components
## Stopped after 66 iterations: Stress nearly unchanged (ratio > sratmax)
1.4) Geographical analysis
Communities quickly change their composition across geographical distances:
1.4.1) Mantel correlograms
Mantel statistic is -significantlly- so low, meaning that the correlation between samples dissimilarity and geographical distances is weak.
##
## Mantel statistic based on Pearson's product-moment correlation
##
## Call:
## mantel(xdis = geo_distances_MP_18S, ydis = tb16_tax_occur_ss16509_no_cero.bray)
##
## Mantel statistic r: 0.1083
## Significance: 0.001
##
## Upper quantiles of permutations (null model):
## 90% 95% 97.5% 99%
## 0.0200 0.0291 0.0359 0.0467
## Permutation: free
## Number of permutations: 999Correlograms:
MP_18s_ss16509_mantel_correl_by_1000km<-mantel.correlog(tb16_tax_occur_ss16509_no_cero.bray, D.geo=geo_distances_MP_18S, break.pts=seq(0,20000, by=1000))
plot(MP_18s_ss16509_mantel_correl_by_1000km)
MP_18s_ss16509_mantel_correl_by_100km<-mantel.correlog(tb16_tax_occur_ss16509_no_cero.bray, D.geo=geo_distances_MP_18S, break.pts=seq(0,20000, by=100))
plot(MP_18s_ss16509_mantel_correl_by_100km)
1.5) Abundance vs. occurence
OTUs distribution according to their percentage of occurence and relative abundance.
- red line: OTUs that occur in more than 80% of the samples.
- blue line: regionally abundant OTUs (> 0.1%).
- green line: regionally rare (< 0.001%).
Regionally abundant OTUs (relative abundance over 0.1%):
## otu_names mean_rabund perc_occur class_B
## 1 OTU_1 0.272434150 100.00000 Prochlorococcus
## 19 OTU_2 0.079469141 100.00000 Prochlorococcus
## 32 OTU_3 0.039445684 100.00000 other_bacteria
## 60 OTU_5 0.019958478 97.80220 other_bacteria
## 74 OTU_6 0.017176112 100.00000 Synechococcus
## 43 OTU_3619 0.017119533 100.00000 other_bacteria
## 91 OTU_8 0.013883869 100.00000 other_bacteria
## 102 OTU_9 0.010413234 100.00000 other_bacteria
## 48 OTU_4 0.009755585 89.01099 other_bacteria
## 85 OTU_7 0.009328911 100.00000 other_bacteria
## 62 OTU_51 0.007644182 100.00000 Prochlorococcus
## 77 OTU_62 0.006768869 100.00000 other_bacteria
## 8 OTU_14 0.006130522 100.00000 other_bacteria
## 7 OTU_13 0.005621309 100.00000 other_bacteria
## 42 OTU_36 0.005459560 48.35165 Prochlorococcus
## 4 OTU_11 0.005357051 100.00000 other_bacteria
## 51 OTU_43 0.005245224 98.90110 other_bacteria
## 63 OTU_52 0.005070162 100.00000 other_bacteria
## 21 OTU_203 0.004783272 81.31868 Synechococcus
## 88 OTU_75 0.004463766 90.10989 Synechococcus
## 2 OTU_10 0.004287372 96.70330 other_bacteria
## 10 OTU_16 0.004263409 94.50549 other_bacteria
## 9 OTU_15 0.003885327 100.00000 other_bacteria
## 6 OTU_12 0.003390092 96.70330 other_bacteria
## 5 OTU_112 0.003313544 84.61538 Prochlorococcus
## 75 OTU_6052 0.003268946 84.61538 other_bacteria
## 28 OTU_27 0.003186407 83.51648 other_bacteria
## 24 OTU_23 0.003173094 96.70330 other_bacteria
## 44 OTU_38 0.003160447 100.00000 other_bacteria
## 97 OTU_8518 0.003129162 86.81319 Prochlorococcus
## 40 OTU_35 0.003090555 91.20879 other_bacteria
## 16 OTU_18 0.002965415 97.80220 other_bacteria
## 13 OTU_17 0.002817644 97.80220 other_bacteria
## 84 OTU_6983 0.002793681 82.41758 Prochlorococcus
## 33 OTU_30 0.002775709 100.00000 other_bacteria
## 37 OTU_33 0.002741761 85.71429 other_bacteria
## 26 OTU_26 0.002640584 97.80220 other_bacteria
## 29 OTU_2754 0.002637256 98.90110 Prochlorococcus
## 25 OTU_24 0.002628603 96.70330 other_bacteria
## 18 OTU_19 0.002609965 95.60440 other_bacteria
## 39 OTU_34 0.002569361 93.40659 other_bacteria
## 22 OTU_21 0.002515444 60.43956 other_bacteria
## 66 OTU_5345 0.002511451 87.91209 Prochlorococcus
## 53 OTU_45 0.002384314 91.20879 other_bacteria
## 72 OTU_5713 0.002192610 87.91209 Prochlorococcus
## 98 OTU_86 0.002167982 97.80220 other_bacteria
## 34 OTU_303 0.002099421 100.00000 other_bacteria
## 90 OTU_77 0.002020876 76.92308 other_bacteria
## 35 OTU_31 0.002017548 91.20879 other_bacteria
## 78 OTU_6249 0.001911046 100.00000 other_bacteria
## 52 OTU_44 0.001904389 94.50549 other_bacteria
## 93 OTU_8015 0.001901061 100.00000 other_bacteria
## 99 OTU_8731 0.001886417 91.20879 other_bacteria
## 38 OTU_3305 0.001879095 82.41758 Prochlorococcus
## 11 OTU_1666 0.001863785 91.20879 Prochlorococcus
## 47 OTU_3997 0.001828506 86.81319 Prochlorococcus
## 20 OTU_20 0.001815859 79.12088 other_bacteria
## 71 OTU_57 0.001789899 100.00000 other_bacteria
## 31 OTU_29 0.001787237 94.50549 other_bacteria
## 15 OTU_178 0.001763940 98.90110 Prochlorococcus
## 45 OTU_39 0.001755286 78.02198 other_bacteria
## 30 OTU_28 0.001753955 71.42857 other_bacteria
## 101 OTU_8904 0.001714017 100.00000 other_bacteria
## 55 OTU_47 0.001692716 96.70330 other_bacteria
## 17 OTU_182 0.001624821 95.60440 other_bacteria
## 65 OTU_53 0.001615502 69.23077 other_bacteria
## 41 OTU_350 0.001594202 96.70330 other_bacteria
## 12 OTU_167 0.001550936 78.02198 Synechococcus
## 50 OTU_42 0.001534960 83.51648 other_bacteria
## 56 OTU_48 0.001467065 82.41758 other_bacteria
## 54 OTU_46 0.001455749 86.81319 other_bacteria
## 27 OTU_269 0.001453752 68.13187 other_bacteria
## 64 OTU_5214 0.001422468 98.90110 other_bacteria
## 49 OTU_40 0.001399170 85.71429 other_bacteria
## 103 OTU_9607 0.001385192 96.70330 other_bacteria
## 96 OTU_8415 0.001375873 100.00000 other_bacteria
## 86 OTU_72 0.001367885 95.60440 other_bacteria
## 61 OTU_5092 0.001357235 82.41758 other_bacteria
## 95 OTU_836 0.001337932 95.60440 Prochlorococcus
## 14 OTU_170 0.001290006 85.71429 Prochlorococcus
## 70 OTU_5677 0.001268705 98.90110 other_bacteria
## 87 OTU_73 0.001235423 19.78022 other_bacteria
## 3 OTU_101 0.001216786 69.23077 other_bacteria
## 67 OTU_54 0.001211460 91.20879 other_bacteria
## 58 OTU_49 0.001192823 89.01099 other_bacteria
## 68 OTU_55 0.001185501 60.43956 other_bacteria
## 46 OTU_396 0.001164866 100.00000 other_bacteria
## 69 OTU_5631 0.001161538 17.58242 Synechococcus
## 80 OTU_63 0.001151553 74.72527 other_bacteria
## 76 OTU_61 0.001148890 100.00000 other_bacteria
## 59 OTU_497 0.001148890 32.96703 other_bacteria
## 81 OTU_65 0.001136243 71.42857 other_bacteria
## 36 OTU_32 0.001124262 74.72527 other_bacteria
## 83 OTU_69 0.001121599 51.64835 other_bacteria
## 94 OTU_8316 0.001117606 89.01099 Prochlorococcus
## 23 OTU_22 0.001110284 87.91209 other_bacteria
## 89 OTU_7628 0.001098302 52.74725 Prochlorococcus
## 57 OTU_4850 0.001060361 90.10989 Prochlorococcus
## 73 OTU_59 0.001039060 91.20879 other_bacteria
## 92 OTU_80 0.001033070 41.75824 other_bacteria
## 79 OTU_627 0.001025082 98.90110 other_bacteria
## 100 OTU_89 0.001016429 85.71429 other_bacteria
## 82 OTU_6798 0.001002450 87.91209 other_bacteria
## SILVA_classif
## 1 KC002097.1.1314_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_unidentified_marine_bacterioplankton
## 19 KM520635.1.1287_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 32 AACY020285848.922.2246_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_marine_metagenome
## 60 KC001782.1.1355_Bacteria_Actinobacteria_Acidimicrobiia_Acidimicrobiales_OM1_clade_Candidatus_Actinomarina_unidentified_marine_bacterioplankton
## 74 KC000519.1.1314_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_unidentified_marine_bacterioplankton
## 43 AACY023868415.1.1427_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_marine_metagenome
## 91 KC002744.1.1344_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## 102 KC002796.1.1323_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_2_unidentified_marine_bacterioplankton
## 48 KJ590614.1.1421_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodobacterales_Rhodobacteraceae_Sulfitobacter_uncultured_bacterium
## 85 KC001931.1.1353_Bacteria_Actinobacteria_Acidimicrobiia_Acidimicrobiales_OM1_clade_Candidatus_Actinomarina_unidentified_marine_bacterioplankton
## 62 JX945368.1.1448_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 77 KF786428.1.1342_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_SAR11_cluster_alpha_proteobacterium
## 8 DQ009267.1.1949_Bacteria_Proteobacteria_Alphaproteobacteria_Rickettsiales_SAR116_clade_uncultured_marine_bacterium
## 7 JX945365.1.1423_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodobacterales_Rhodobacteraceae_uncultured_uncultured_bacterium
## 42 HQ233040.1.1357_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_Prochlorococcus_sp
## 4 DQ009111.1.2063_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS2b_marine_group_uncultured_marine_bacterium
## 51 KC000418.1.1315_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## 63 KC002212.1.1315_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## 21 KC002165.1.1315_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_unidentified_marine_bacterioplankton
## 88 GU061737.1.1446_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_bacterium
## 2 KJ549180.1.1447_Bacteria_Proteobacteria_Alphaproteobacteria_Sphingomonadales_Erythrobacteraceae_Erythrobacter_uncultured_bacterium
## 10 AACY020257759.244.1709_Bacteria_Proteobacteria_Alphaproteobacteria_Rickettsiales_SAR116_clade_marine_metagenome
## 9 EU804112.1.1492_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS5_marine_group_uncultured_bacterium
## 6 JN986244.1.1428_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodobacterales_Rhodobacteraceae_uncultured_uncultured_bacterium
## 5 EU237289.1.1306_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 75 EU802327.1.1487_Bacteria_Actinobacteria_Acidimicrobiia_Acidimicrobiales_OM1_clade_Candidatus_Actinomarina_uncultured_bacterium
## 28 EU802512.1.1493_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS4_marine_group_uncultured_bacterium
## 24 AACY023498084.1.1233_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS4_marine_group_marine_metagenome
## 44 KC001705.1.1365_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_SAR86_clade_unidentified_marine_bacterioplankton
## 97 KC002188.1.1314_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_unidentified_marine_bacterioplankton
## 40 EU804152.1.1492_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS4_marine_group_uncultured_bacterium
## 16 KC001557.1.1292_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodobacterales_Rhodobacteraceae_uncultured_unidentified_marine_bacterioplankton
## 13 EU237459.1.1302_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirillales_Rhodospirillaceae_AEGEAN-169_marine_group_uncultured_bacterium
## 84 KC001872.1.1314_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_unidentified_marine_bacterioplankton
## 33 JN986006.1.1452_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_4_uncultured_bacterium
## 37 DQ009141.1.1996_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_SAR86_clade_uncultured_marine_bacterium
## 26 KC002130.1.1290_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodobacterales_Rhodobacteraceae_uncultured_unidentified_marine_bacterioplankton
## 29 HQ233043.1.1357_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_Prochlorococcus_sp
## 25 EU802705.1.1252_Bacteria_Bacteroidetes_Cytophagia_Cytophagales_Flammeovirgaceae_Marinoscillum_uncultured_bacterium
## 18 KJ549185.1.1449_Bacteria_Proteobacteria_Alphaproteobacteria_Sphingomonadales_Erythrobacteraceae_Erythrobacter_uncultured_bacterium
## 39 FN433299.1.1479_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS2b_marine_group_uncultured_Flavobacteriia_bacterium
## 22 DQ009121.1.1748_Bacteria_Actinobacteria_Acidimicrobiia_Acidimicrobiales_OM1_clade_Candidatus_Actinomarina_uncultured_marine_bacterium
## 66 KC002668.1.1343_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_unidentified_marine_bacterioplankton
## 53 KC002674.1.1343_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## 72 JX945368.1.1448_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 98 JN985994.1.1438_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 34 EU802406.1.1257_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 90 FN433412.1.1496_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS4_marine_group_uncultured_Flavobacteriia_bacterium
## 35 AACY020563509.792.2305_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_SAR86_clade_marine_metagenome
## 78 KC002895.1.1345_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## 52 AQSI01000003.54241.55782_Bacteria_Marinimicrobia__SAR406_clade__Marinimicrobia_bacterium_SCGC_AAA298-D23
## 93 EU804784.1.1433_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 99 KF786624.1.1388_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS2b_marine_group_uncultured_Flavobacteriales_bacterium
## 38 JN986032.1.1449_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 11 AY664087.1.1207_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_Prochlorococcus_sp
## 47 JN986032.1.1449_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 20 KC003455.1.1350_Bacteria_Proteobacteria_Gammaproteobacteria_Alteromonadales_Alteromonadaceae_Alteromonas_unidentified_marine_bacterioplankton
## 71 EU805317.1.1450_Bacteria_Proteobacteria_Alphaproteobacteria_Rickettsiales_SAR116_clade_uncultured_bacterium
## 31 EU804109.1.1485_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_NS9_marine_group_uncultured_bacterium
## 15 JNAU01000004.222174.223638_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_Prochlorococcus_sp._MIT_0601
## 45 KC000407.1.1363_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_Formosa_unidentified_marine_bacterioplankton
## 30 JX105591.1.1377_Bacteria_Actinobacteria_Actinobacteria_Corynebacteriales_Nocardiaceae_Rhodococcus_uncultured_bacterium
## 101 EU804476.1.1440_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 55 JN986342.1.1465_Bacteria_Proteobacteria_Alphaproteobacteria_Rickettsiales_S25-593_uncultured_bacterium
## 17 DQ396183.1.1451_Bacteria_Proteobacteria_Alphaproteobacteria_Sphingomonadales_Erythrobacteraceae_Erythrobacter_uncultured_organism
## 65 AACY020549891.3846.5359_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_SAR86_clade_marine_metagenome
## 41 KC002791.1.1322_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## 12 JN166214.1.1446_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_marine_microorganism
## 50 EU804751.1.1482_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_NS7_marine_group_uncultured_bacterium
## 56 AACY020562322.3851.5364_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_SAR86_clade_marine_metagenome
## 54 EU803106.1.1287_Bacteria_Proteobacteria_Deltaproteobacteria_SAR324_clade_Marine_group_B__uncultured_bacterium
## 27 JQ516674.1.1506_Bacteria_Actinobacteria_Acidimicrobiia_Acidimicrobiales_OM1_clade_Candidatus_Actinomarina_uncultured_actinobacterium
## 64 EF572784.1.1439_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 49 KF786431.1.1388_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS2b_marine_group_uncultured_Flavobacteriales_bacterium
## 103 EU804974.1.1439_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 96 GQ346738.1.1322_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_alpha_proteobacterium
## 86 AACY020555764.489.1966_Bacteria_Proteobacteria_Alphaproteobacteria_OCS116_clade_marine_metagenome
## 61 JX945339.1.1492_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS5_marine_group_uncultured_bacterium
## 95 KM520431.1.1266_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 14 KC002188.1.1314_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_unidentified_marine_bacterioplankton
## 70 KC294824.1.1401_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 87 AACY020462030.661.2167_Bacteria_Actinobacteria_Acidimicrobiia_Acidimicrobiales_OM1_clade_Candidatus_Actinomarina_marine_metagenome
## 3 JX526770.1.1401_Bacteria_Proteobacteria_Gammaproteobacteria_Thiotrichales_Thiotrichaceae_Thiothrix_uncultured_proteobacterium
## 67 AACY020481938.3418.4929_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_SAR86_clade_marine_metagenome
## 58 DQ009125.1.1942_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_SAR86_clade_uncultured_marine_bacterium
## 68 FQ032819.21712.23225_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS4_marine_group_uncultured_Flavobacteriia_bacterium
## 46 KC294823.1.1400_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 69 JN832945.1.1352_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_bacterium
## 80 JQ013156.1.1423_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodobacterales_Rhodobacteraceae_Ascidiaceihabitans_uncultured_bacterium
## 76 AACY020490277.719.2228_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS5_marine_group_marine_metagenome
## 59 KC811143.18830.20338_Bacteria_Actinobacteria_Acidimicrobiia_Acidimicrobiales_OM1_clade_Candidatus_Actinomarina_Candidatus_Actinomarina_minuta
## 81 DQ009089.1.1878_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_NS9_marine_group_uncultured_marine_bacterium
## 36 HQ622550.1.1449_Bacteria_Proteobacteria_Alphaproteobacteria_Rhizobiales_Aurantimonadaceae_Fulvimarina_Rhizobiales_bacterium_8047
## 83 ATUR01000005.1108.2578_Bacteria_Proteobacteria_Alphaproteobacteria_Sphingomonadales_Sphingomonadaceae_Sphingopyxis_Sphingopyxis_baekryungensis_DSM_16222
## 94 KC002188.1.1314_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_unidentified_marine_bacterioplankton
## 23 JQ032339.1.1400_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_Halomonadaceae_Halomonas_uncultured_bacterium
## 89 HQ233039.1.1357_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_Prochlorococcus_sp
## 57 JX945368.1.1448_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 73 EU795293.31983.33492_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS5_marine_group_uncultured_bacterium_HF0010_31F02
## 92 KC001532.1.1292_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodobacterales_Rhodobacteraceae_Ruegeria_unidentified_marine_bacterioplankton
## 79 EU802825.1.1438_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 100 JN018663.1.1390_Bacteria_Proteobacteria_Gammaproteobacteria_KI89A_clade_uncultured_bacterium
## 82 KC003176.1.1343_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## PhytoREF_classif
## 1 CyanoDB_KC003178.1.1230_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_unidentified_unidentified_marine
## 19 CyanoDB_X52169.1.1473_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 32 <NA>
## 60 <NA>
## 74 CyanoDB_JX945359.1.1444_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 43 <NA>
## 91 <NA>
## 102 <NA>
## 48 <NA>
## 85 <NA>
## 62 CyanoDB_JX945368.1.1448_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 77 <NA>
## 8 <NA>
## 7 <NA>
## 42 CyanoDB_KC003178.1.1230_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_unidentified_unidentified_marine
## 4 <NA>
## 51 <NA>
## 63 <NA>
## 21 CyanoDB_FJ999613.1.1344_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 88 CyanoDB_EF574993.1.1450_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 2 <NA>
## 10 <NA>
## 9 <NA>
## 6 <NA>
## 5 CyanoDB_JN547438.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 75 <NA>
## 28 <NA>
## 24 <NA>
## 44 <NA>
## 97 CyanoDB_JN547438.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 40 <NA>
## 16 <NA>
## 13 <NA>
## 84 CyanoDB_KC003178.1.1230_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_unidentified_unidentified_marine
## 33 <NA>
## 37 <NA>
## 26 <NA>
## 29 CyanoDB_X52169.1.1473_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 25 <NA>
## 18 <NA>
## 39 <NA>
## 22 <NA>
## 66 CyanoDB_EU802376.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 53 <NA>
## 72 CyanoDB_JX945368.1.1448_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 98 <NA>
## 34 <NA>
## 90 <NA>
## 35 <NA>
## 78 <NA>
## 52 <NA>
## 93 <NA>
## 99 <NA>
## 38 CyanoDB_AY664087.1.1207_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 11 CyanoDB_AY664087.1.1207_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 47 CyanoDB_AY664087.1.1207_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 20 <NA>
## 71 <NA>
## 31 <NA>
## 15 CyanoDB_JN547438.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 45 <NA>
## 30 <NA>
## 101 <NA>
## 55 <NA>
## 17 <NA>
## 65 <NA>
## 41 <NA>
## 12 CyanoDB_EF574993.1.1450_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 50 <NA>
## 56 <NA>
## 54 <NA>
## 27 <NA>
## 64 <NA>
## 49 <NA>
## 103 <NA>
## 96 <NA>
## 86 <NA>
## 61 <NA>
## 95 CyanoDB_JN547438.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 14 CyanoDB_JN547438.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 70 <NA>
## 87 <NA>
## 3 <NA>
## 67 <NA>
## 58 <NA>
## 68 <NA>
## 46 <NA>
## 69 CyanoDB_HQ672155.1.1438_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 80 <NA>
## 76 <NA>
## 59 <NA>
## 81 <NA>
## 36 <NA>
## 83 <NA>
## 94 CyanoDB_JN547438.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 23 <NA>
## 89 CyanoDB_X52169.1.1473_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 57 CyanoDB_JX945368.1.1448_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 73 <NA>
## 92 <NA>
## 79 <NA>
## 100 <NA>
## 82 <NA>Number and roportion of regionally abundant OTUs (%):
## [1] 103## [1] 1.260247
Cosmopolitan OTUs (relative abundance over 0.1% and occurence in more than 80% of samples):
## otu_names mean_rabund perc_occur class_B
## 1 OTU_1 0.272434150 100.00000 Prochlorococcus
## 17 OTU_2 0.079469141 100.00000 Prochlorococcus
## 26 OTU_3 0.039445684 100.00000 other_bacteria
## 61 OTU_6 0.017176112 100.00000 Synechococcus
## 35 OTU_3619 0.017119533 100.00000 other_bacteria
## 72 OTU_8 0.013883869 100.00000 other_bacteria
## 82 OTU_9 0.010413234 100.00000 other_bacteria
## 69 OTU_7 0.009328911 100.00000 other_bacteria
## 52 OTU_51 0.007644182 100.00000 Prochlorococcus
## 64 OTU_62 0.006768869 100.00000 other_bacteria
## 7 OTU_14 0.006130522 100.00000 other_bacteria
## 6 OTU_13 0.005621309 100.00000 other_bacteria
## 3 OTU_11 0.005357051 100.00000 other_bacteria
## 53 OTU_52 0.005070162 100.00000 other_bacteria
## 8 OTU_15 0.003885327 100.00000 other_bacteria
## 36 OTU_38 0.003160447 100.00000 other_bacteria
## 27 OTU_30 0.002775709 100.00000 other_bacteria
## 28 OTU_303 0.002099421 100.00000 other_bacteria
## 65 OTU_6249 0.001911046 100.00000 other_bacteria
## 73 OTU_8015 0.001901061 100.00000 other_bacteria
## 58 OTU_57 0.001789899 100.00000 other_bacteria
## 81 OTU_8904 0.001714017 100.00000 other_bacteria
## 76 OTU_8415 0.001375873 100.00000 other_bacteria
## 37 OTU_396 0.001164866 100.00000 other_bacteria
## 63 OTU_61 0.001148890 100.00000 other_bacteria
## 42 OTU_43 0.005245224 98.90110 other_bacteria
## 24 OTU_2754 0.002637256 98.90110 Prochlorococcus
## 13 OTU_178 0.001763940 98.90110 Prochlorococcus
## 54 OTU_5214 0.001422468 98.90110 other_bacteria
## 57 OTU_5677 0.001268705 98.90110 other_bacteria
## 66 OTU_627 0.001025082 98.90110 other_bacteria
## 50 OTU_5 0.019958478 97.80220 other_bacteria
## 14 OTU_18 0.002965415 97.80220 other_bacteria
## 11 OTU_17 0.002817644 97.80220 other_bacteria
## 22 OTU_26 0.002640584 97.80220 other_bacteria
## 78 OTU_86 0.002167982 97.80220 other_bacteria
## 2 OTU_10 0.004287372 96.70330 other_bacteria
## 5 OTU_12 0.003390092 96.70330 other_bacteria
## 20 OTU_23 0.003173094 96.70330 other_bacteria
## 21 OTU_24 0.002628603 96.70330 other_bacteria
## 46 OTU_47 0.001692716 96.70330 other_bacteria
## 34 OTU_350 0.001594202 96.70330 other_bacteria
## 83 OTU_9607 0.001385192 96.70330 other_bacteria
## 16 OTU_19 0.002609965 95.60440 other_bacteria
## 15 OTU_182 0.001624821 95.60440 other_bacteria
## 70 OTU_72 0.001367885 95.60440 other_bacteria
## 75 OTU_836 0.001337932 95.60440 Prochlorococcus
## 9 OTU_16 0.004263409 94.50549 other_bacteria
## 43 OTU_44 0.001904389 94.50549 other_bacteria
## 25 OTU_29 0.001787237 94.50549 other_bacteria
## 32 OTU_34 0.002569361 93.40659 other_bacteria
## 33 OTU_35 0.003090555 91.20879 other_bacteria
## 44 OTU_45 0.002384314 91.20879 other_bacteria
## 29 OTU_31 0.002017548 91.20879 other_bacteria
## 79 OTU_8731 0.001886417 91.20879 other_bacteria
## 10 OTU_1666 0.001863785 91.20879 Prochlorococcus
## 56 OTU_54 0.001211460 91.20879 other_bacteria
## 60 OTU_59 0.001039060 91.20879 other_bacteria
## 71 OTU_75 0.004463766 90.10989 Synechococcus
## 48 OTU_4850 0.001060361 90.10989 Prochlorococcus
## 39 OTU_4 0.009755585 89.01099 other_bacteria
## 49 OTU_49 0.001192823 89.01099 other_bacteria
## 74 OTU_8316 0.001117606 89.01099 Prochlorococcus
## 55 OTU_5345 0.002511451 87.91209 Prochlorococcus
## 59 OTU_5713 0.002192610 87.91209 Prochlorococcus
## 19 OTU_22 0.001110284 87.91209 other_bacteria
## 67 OTU_6798 0.001002450 87.91209 other_bacteria
## 77 OTU_8518 0.003129162 86.81319 Prochlorococcus
## 38 OTU_3997 0.001828506 86.81319 Prochlorococcus
## 45 OTU_46 0.001455749 86.81319 other_bacteria
## 30 OTU_33 0.002741761 85.71429 other_bacteria
## 40 OTU_40 0.001399170 85.71429 other_bacteria
## 12 OTU_170 0.001290006 85.71429 Prochlorococcus
## 80 OTU_89 0.001016429 85.71429 other_bacteria
## 4 OTU_112 0.003313544 84.61538 Prochlorococcus
## 62 OTU_6052 0.003268946 84.61538 other_bacteria
## 23 OTU_27 0.003186407 83.51648 other_bacteria
## 41 OTU_42 0.001534960 83.51648 other_bacteria
## 68 OTU_6983 0.002793681 82.41758 Prochlorococcus
## 31 OTU_3305 0.001879095 82.41758 Prochlorococcus
## 47 OTU_48 0.001467065 82.41758 other_bacteria
## 51 OTU_5092 0.001357235 82.41758 other_bacteria
## 18 OTU_203 0.004783272 81.31868 Synechococcus
## SILVA_classif
## 1 KC002097.1.1314_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_unidentified_marine_bacterioplankton
## 17 KM520635.1.1287_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 26 AACY020285848.922.2246_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_marine_metagenome
## 61 KC000519.1.1314_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_unidentified_marine_bacterioplankton
## 35 AACY023868415.1.1427_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_marine_metagenome
## 72 KC002744.1.1344_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## 82 KC002796.1.1323_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_2_unidentified_marine_bacterioplankton
## 69 KC001931.1.1353_Bacteria_Actinobacteria_Acidimicrobiia_Acidimicrobiales_OM1_clade_Candidatus_Actinomarina_unidentified_marine_bacterioplankton
## 52 JX945368.1.1448_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 64 KF786428.1.1342_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_SAR11_cluster_alpha_proteobacterium
## 7 DQ009267.1.1949_Bacteria_Proteobacteria_Alphaproteobacteria_Rickettsiales_SAR116_clade_uncultured_marine_bacterium
## 6 JX945365.1.1423_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodobacterales_Rhodobacteraceae_uncultured_uncultured_bacterium
## 3 DQ009111.1.2063_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS2b_marine_group_uncultured_marine_bacterium
## 53 KC002212.1.1315_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## 8 EU804112.1.1492_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS5_marine_group_uncultured_bacterium
## 36 KC001705.1.1365_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_SAR86_clade_unidentified_marine_bacterioplankton
## 27 JN986006.1.1452_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_4_uncultured_bacterium
## 28 EU802406.1.1257_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 65 KC002895.1.1345_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## 73 EU804784.1.1433_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 58 EU805317.1.1450_Bacteria_Proteobacteria_Alphaproteobacteria_Rickettsiales_SAR116_clade_uncultured_bacterium
## 81 EU804476.1.1440_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 76 GQ346738.1.1322_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_alpha_proteobacterium
## 37 KC294823.1.1400_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 63 AACY020490277.719.2228_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS5_marine_group_marine_metagenome
## 42 KC000418.1.1315_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## 24 HQ233043.1.1357_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_Prochlorococcus_sp
## 13 JNAU01000004.222174.223638_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_Prochlorococcus_sp._MIT_0601
## 54 EF572784.1.1439_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 57 KC294824.1.1401_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 66 EU802825.1.1438_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 50 KC001782.1.1355_Bacteria_Actinobacteria_Acidimicrobiia_Acidimicrobiales_OM1_clade_Candidatus_Actinomarina_unidentified_marine_bacterioplankton
## 14 KC001557.1.1292_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodobacterales_Rhodobacteraceae_uncultured_unidentified_marine_bacterioplankton
## 11 EU237459.1.1302_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodospirillales_Rhodospirillaceae_AEGEAN-169_marine_group_uncultured_bacterium
## 22 KC002130.1.1290_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodobacterales_Rhodobacteraceae_uncultured_unidentified_marine_bacterioplankton
## 78 JN985994.1.1438_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 2 KJ549180.1.1447_Bacteria_Proteobacteria_Alphaproteobacteria_Sphingomonadales_Erythrobacteraceae_Erythrobacter_uncultured_bacterium
## 5 JN986244.1.1428_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodobacterales_Rhodobacteraceae_uncultured_uncultured_bacterium
## 20 AACY023498084.1.1233_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS4_marine_group_marine_metagenome
## 21 EU802705.1.1252_Bacteria_Bacteroidetes_Cytophagia_Cytophagales_Flammeovirgaceae_Marinoscillum_uncultured_bacterium
## 46 JN986342.1.1465_Bacteria_Proteobacteria_Alphaproteobacteria_Rickettsiales_S25-593_uncultured_bacterium
## 34 KC002791.1.1322_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## 83 EU804974.1.1439_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_uncultured_bacterium
## 16 KJ549185.1.1449_Bacteria_Proteobacteria_Alphaproteobacteria_Sphingomonadales_Erythrobacteraceae_Erythrobacter_uncultured_bacterium
## 15 DQ396183.1.1451_Bacteria_Proteobacteria_Alphaproteobacteria_Sphingomonadales_Erythrobacteraceae_Erythrobacter_uncultured_organism
## 70 AACY020555764.489.1966_Bacteria_Proteobacteria_Alphaproteobacteria_OCS116_clade_marine_metagenome
## 75 KM520431.1.1266_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 9 AACY020257759.244.1709_Bacteria_Proteobacteria_Alphaproteobacteria_Rickettsiales_SAR116_clade_marine_metagenome
## 43 AQSI01000003.54241.55782_Bacteria_Marinimicrobia__SAR406_clade__Marinimicrobia_bacterium_SCGC_AAA298-D23
## 25 EU804109.1.1485_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_NS9_marine_group_uncultured_bacterium
## 32 FN433299.1.1479_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS2b_marine_group_uncultured_Flavobacteriia_bacterium
## 33 EU804152.1.1492_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS4_marine_group_uncultured_bacterium
## 44 KC002674.1.1343_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## 29 AACY020563509.792.2305_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_SAR86_clade_marine_metagenome
## 79 KF786624.1.1388_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS2b_marine_group_uncultured_Flavobacteriales_bacterium
## 10 AY664087.1.1207_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_Prochlorococcus_sp
## 56 AACY020481938.3418.4929_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_SAR86_clade_marine_metagenome
## 60 EU795293.31983.33492_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS5_marine_group_uncultured_bacterium_HF0010_31F02
## 71 GU061737.1.1446_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_bacterium
## 48 JX945368.1.1448_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 39 KJ590614.1.1421_Bacteria_Proteobacteria_Alphaproteobacteria_Rhodobacterales_Rhodobacteraceae_Sulfitobacter_uncultured_bacterium
## 49 DQ009125.1.1942_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_SAR86_clade_uncultured_marine_bacterium
## 74 KC002188.1.1314_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_unidentified_marine_bacterioplankton
## 55 KC002668.1.1343_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_unidentified_marine_bacterioplankton
## 59 JX945368.1.1448_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 19 JQ032339.1.1400_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_Halomonadaceae_Halomonas_uncultured_bacterium
## 67 KC003176.1.1343_Bacteria_Proteobacteria_Alphaproteobacteria_SAR11_clade_Surface_1_unidentified_marine_bacterioplankton
## 77 KC002188.1.1314_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_unidentified_marine_bacterioplankton
## 38 JN986032.1.1449_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 45 EU803106.1.1287_Bacteria_Proteobacteria_Deltaproteobacteria_SAR324_clade_Marine_group_B__uncultured_bacterium
## 30 DQ009141.1.1996_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_SAR86_clade_uncultured_marine_bacterium
## 40 KF786431.1.1388_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS2b_marine_group_uncultured_Flavobacteriales_bacterium
## 12 KC002188.1.1314_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_unidentified_marine_bacterioplankton
## 80 JN018663.1.1390_Bacteria_Proteobacteria_Gammaproteobacteria_KI89A_clade_uncultured_bacterium
## 4 EU237289.1.1306_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 62 EU802327.1.1487_Bacteria_Actinobacteria_Acidimicrobiia_Acidimicrobiales_OM1_clade_Candidatus_Actinomarina_uncultured_bacterium
## 23 EU802512.1.1493_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS4_marine_group_uncultured_bacterium
## 41 EU804751.1.1482_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_NS7_marine_group_uncultured_bacterium
## 68 KC001872.1.1314_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_unidentified_marine_bacterioplankton
## 31 JN986032.1.1449_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_bacterium
## 47 AACY020562322.3851.5364_Bacteria_Proteobacteria_Gammaproteobacteria_Oceanospirillales_SAR86_clade_marine_metagenome
## 51 JX945339.1.1492_Bacteria_Bacteroidetes_Flavobacteriia_Flavobacteriales_Flavobacteriaceae_NS5_marine_group_uncultured_bacterium
## 18 KC002165.1.1315_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_unidentified_marine_bacterioplankton
## PhytoREF_classif
## 1 CyanoDB_KC003178.1.1230_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_unidentified_unidentified_marine
## 17 CyanoDB_X52169.1.1473_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 26 <NA>
## 61 CyanoDB_JX945359.1.1444_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 35 <NA>
## 72 <NA>
## 82 <NA>
## 69 <NA>
## 52 CyanoDB_JX945368.1.1448_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 64 <NA>
## 7 <NA>
## 6 <NA>
## 3 <NA>
## 53 <NA>
## 8 <NA>
## 36 <NA>
## 27 <NA>
## 28 <NA>
## 65 <NA>
## 73 <NA>
## 58 <NA>
## 81 <NA>
## 76 <NA>
## 37 <NA>
## 63 <NA>
## 42 <NA>
## 24 CyanoDB_X52169.1.1473_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 13 CyanoDB_JN547438.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 54 <NA>
## 57 <NA>
## 66 <NA>
## 50 <NA>
## 14 <NA>
## 11 <NA>
## 22 <NA>
## 78 <NA>
## 2 <NA>
## 5 <NA>
## 20 <NA>
## 21 <NA>
## 46 <NA>
## 34 <NA>
## 83 <NA>
## 16 <NA>
## 15 <NA>
## 70 <NA>
## 75 CyanoDB_JN547438.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 9 <NA>
## 43 <NA>
## 25 <NA>
## 32 <NA>
## 33 <NA>
## 44 <NA>
## 29 <NA>
## 79 <NA>
## 10 CyanoDB_AY664087.1.1207_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 56 <NA>
## 60 <NA>
## 71 CyanoDB_EF574993.1.1450_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacterium
## 48 CyanoDB_JX945368.1.1448_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 39 <NA>
## 49 <NA>
## 74 CyanoDB_JN547438.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 55 CyanoDB_EU802376.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 59 CyanoDB_JX945368.1.1448_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_bacterium
## 19 <NA>
## 67 <NA>
## 77 CyanoDB_JN547438.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 38 CyanoDB_AY664087.1.1207_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 45 <NA>
## 30 <NA>
## 40 <NA>
## 12 CyanoDB_JN547438.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 80 <NA>
## 4 CyanoDB_JN547438.1.1447_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 62 <NA>
## 23 <NA>
## 41 <NA>
## 68 CyanoDB_KC003178.1.1230_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_unidentified_unidentified_marine
## 31 CyanoDB_AY664087.1.1207_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Prochlorococcus_uncultured_uncultured_Prochlorococcus
## 47 <NA>
## 51 <NA>
## 18 CyanoDB_FJ999613.1.1344_Bacteria_Cyanobacteria_Cyanobacteria_SubsectionI_FamilyI_Synechococcus_uncultured_uncultured_bacteriumNumber and proportion (%) of cosmopolitan OTUs:
## [1] 83## [1] 1.015539Number and proportion (%) of rare OTUs:
## [1] 4665## [1] 57.078182.6) Taxonomic composition analysis
2.6.1) Normalized data
No. of OTUs and reads of the rearefied dataset:
## [1] 8173## [1] 1502319
Number and proportion (%) of OTUs of phototrophic groups:
## [1] 1832## [1] 22.41527Number and proportion (%) of reads of phototrophic groups:
## [1] 770960## [1] 51.318
Number and proportion (%) of OTUs of non-phototrophic groups:
## [1] 6341## [1] 77.58473Number and proportion (%) of reads of non-phototrophic groups:
## [1] 731359## [1] 48.682
PHOTOTROPHS + HETEROTROPHS
Absolute values
## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 128 11 31
## Bolidophyceae 81 4 41
## Chlorarachniophyceae 13 2 10
## Chlorodendrophyceae 2 1 2
## Cryptophyceae 40 4 18
## Cyanobacteria 752531 1211 91
## Dictyochophyceae 1333 31 88
## Dinophyceae 256 14 56
## Eustigmatophyceae 125 6 49
## Mamiellophyceae 860 16 26
## Pelagophyceae 399 19 65
## Prasinophyceae_clade-IX 578 18 73
## Prasinophyceae_clade-VII 293 15 34
## Prymnesiophyceae 8845 314 91
## Pyramimonadaceae 32 3 11
## Rappemonads 34 7 24
## Trebouxiophyceae 2 1 1
## other_Prasinophyceae 13 2 10
## other_bacteria 731359 6341 91
## other_plastids 5395 153 91
Relative values
## reads_per_class OTUs_per_class samples_per_class
## 100.0000 100.0000 992.3077## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 8.520161e-03 0.13458950 34.065934
## Bolidophyceae 5.391664e-03 0.04894164 45.054945
## Chlorarachniophyceae 8.653289e-04 0.02447082 10.989011
## Chlorodendrophyceae 1.331275e-04 0.01223541 2.197802
## Cryptophyceae 2.662550e-03 0.04894164 19.780220
## Cyanobacteria 5.009129e+01 14.81708063 100.000000
## Dictyochophyceae 8.872949e-02 0.37929769 96.703297
## Dinophyceae 1.704032e-02 0.17129573 61.538462
## Eustigmatophyceae 8.320470e-03 0.07341246 53.846154
## Mamiellophyceae 5.724483e-02 0.19576655 28.571429
## Pelagophyceae 2.655894e-02 0.23247278 71.428571
## Prasinophyceae_clade-IX 3.847385e-02 0.22023737 80.219780
## Prasinophyceae_clade-VII 1.950318e-02 0.18353114 37.362637
## Prymnesiophyceae 5.887564e-01 3.84191851 100.000000
## Pyramimonadaceae 2.130040e-03 0.03670623 12.087912
## Rappemonads 2.263168e-03 0.08564786 26.373626
## Trebouxiophyceae 1.331275e-04 0.01223541 1.098901
## other_Prasinophyceae 8.653289e-04 0.02447082 10.989011
## other_bacteria 4.868200e+01 77.58473021 100.000000
## other_plastids 3.591115e-01 1.87201762 100.000000
Reads per class vs. OTUs per class:
Reads per class vs. samples in which they occurr:
PHOTOTROPHS
Absolute values
## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 128 11 31
## Bolidophyceae 81 4 41
## Chlorarachniophyceae 13 2 10
## Chlorodendrophyceae 2 1 2
## Cryptophyceae 40 4 18
## Cyanobacteria 752531 1211 91
## Dictyochophyceae 1333 31 88
## Dinophyceae 256 14 56
## Eustigmatophyceae 125 6 49
## Mamiellophyceae 860 16 26
## Pelagophyceae 399 19 65
## Prasinophyceae_clade-IX 578 18 73
## Prasinophyceae_clade-VII 293 15 34
## Prymnesiophyceae 8845 314 91
## Pyramimonadaceae 32 3 11
## Rappemonads 34 7 24
## Trebouxiophyceae 2 1 1
## other_Prasinophyceae 13 2 10
## other_plastids 5395 153 91
Relative values
## reads_per_class OTUs_per_class samples_per_class
## 100.0000 100.0000 892.3077## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 1.660268e-02 0.60043668 34.065934
## Bolidophyceae 1.050638e-02 0.21834061 45.054945
## Chlorarachniophyceae 1.686209e-03 0.10917031 10.989011
## Chlorodendrophyceae 2.594168e-04 0.05458515 2.197802
## Cryptophyceae 5.188337e-03 0.21834061 19.780220
## Cyanobacteria 9.760960e+01 66.10262009 100.000000
## Dictyochophyceae 1.729013e-01 1.69213974 96.703297
## Dinophyceae 3.320535e-02 0.76419214 61.538462
## Eustigmatophyceae 1.621355e-02 0.32751092 53.846154
## Mamiellophyceae 1.115492e-01 0.87336245 28.571429
## Pelagophyceae 5.175366e-02 1.03711790 71.428571
## Prasinophyceae_clade-IX 7.497146e-02 0.98253275 80.219780
## Prasinophyceae_clade-VII 3.800457e-02 0.81877729 37.362637
## Prymnesiophyceae 1.147271e+00 17.13973799 100.000000
## Pyramimonadaceae 4.150669e-03 0.16375546 12.087912
## Rappemonads 4.410086e-03 0.38209607 26.373626
## Trebouxiophyceae 2.594168e-04 0.05458515 1.098901
## other_Prasinophyceae 1.686209e-03 0.10917031 10.989011
## other_plastids 6.997769e-01 8.35152838 100.000000
Reads per class vs. OTUs per class:
Reads per class vs. samples in which they occurr:
Absolute values of cyanobacteria groups richness and abundance:
## reads_per_class OTUs_per_class
## Prochlorococcus 688078 979
## Synechococcus 61311 162
## other_cyanobacteria 3142 70Relative values of Cyanobacteria groups richness and abundance:
## reads_per_class OTUs_per_class
## Prochlorococcus 91.4351701 80.842279
## Synechococcus 8.1473056 13.377374
## Other cyanobacteria 0.4175243 5.780347
PROTISTS
## [1] 621## [1] 18429Absolute values
## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 128 11 31
## Bolidophyceae 81 4 41
## Chlorarachniophyceae 13 2 10
## Chlorodendrophyceae 2 1 2
## Cryptophyceae 40 4 18
## Dictyochophyceae 1333 31 88
## Dinophyceae 256 14 56
## Eustigmatophyceae 125 6 49
## Mamiellophyceae 860 16 26
## Pelagophyceae 399 19 65
## Prasinophyceae_clade-IX 578 18 73
## Prasinophyceae_clade-VII 293 15 34
## Prymnesiophyceae 8845 314 91
## Pyramimonadaceae 32 3 11
## Rappemonads 34 7 24
## Trebouxiophyceae 2 1 1
## other_Prasinophyceae 13 2 10
## other_plastids 5395 153 91
Relative values
## reads_per_class OTUs_per_class samples_per_class
## 100.0000 100.0000 792.3077## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 0.69455749 1.7713366 34.065934
## Bolidophyceae 0.43952466 0.6441224 45.054945
## Chlorarachniophyceae 0.07054100 0.3220612 10.989011
## Chlorodendrophyceae 0.01085246 0.1610306 2.197802
## Cryptophyceae 0.21704922 0.6441224 19.780220
## Dictyochophyceae 7.23316512 4.9919485 96.703297
## Dinophyceae 1.38911498 2.2544283 61.538462
## Eustigmatophyceae 0.67827880 0.9661836 53.846154
## Mamiellophyceae 4.66655814 2.5764895 28.571429
## Pelagophyceae 2.16506593 3.0595813 71.428571
## Prasinophyceae_clade-IX 3.13636117 2.8985507 80.219780
## Prasinophyceae_clade-VII 1.58988551 2.4154589 37.362637
## Prymnesiophyceae 47.99500787 50.5636071 100.000000
## Pyramimonadaceae 0.17363937 0.4830918 12.087912
## Rappemonads 0.18449183 1.1272142 26.373626
## Trebouxiophyceae 0.01085246 0.1610306 1.098901
## other_Prasinophyceae 0.07054100 0.3220612 10.989011
## other_plastids 29.27451300 24.6376812 100.000000
Reads per class vs. OTUs per class:
Reads per class vs. samples in which they occurr:
2.6.2) Non-rarefied data
No. of OTUs and reads of the rearefied dataset:
## [1] 8881## [1] 4745946
Number and proportion (%) of OTUs of phototrophic groups:
## [1] 1952## [1] 21.97951Number and proportion (%) of reads of phototrophic groups:
## [1] 1166677## [1] 52.79046
Number and proportion (%) of OTUs of non-phototrophic groups:
## [1] 6929## [1] 78.02049Number and proportion (%) of reads of non-phototrophic groups:
## [1] 1043338## [1] 47.20954
PHOTOTROPHS + HETEROTROPHS
Absolute values
## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 450 14 42
## Bolidophyceae 271 4 61
## Chlorarachniophyceae 25 2 16
## Chlorodendrophyceae 8 1 5
## Cryptophyceae 103 6 24
## Cyanobacteria 2449889 1278 91
## Dictyochophyceae 4003 31 89
## Dinophyceae 819 17 73
## Eustigmatophyceae 369 6 56
## Mamiellophyceae 1248 16 34
## Pelagophyceae 1076 19 75
## Prasinophyceae_clade-IX 1785 23 80
## Prasinophyceae_clade-VII 923 16 49
## Prymnesiophyceae 26832 336 91
## Pyramimonadaceae 51 3 17
## Rappemonads 136 7 41
## Trebouxiophyceae 2 1 1
## other_Prasinophyceae 27 2 16
## other_bacteria 2241360 6929 91
## other_plastids 16569 170 91
Relative values
## reads_per_class OTUs_per_class samples_per_class
## 100.000 100.000 1146.154## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 9.481777e-03 0.15763991 46.153846
## Bolidophyceae 5.710137e-03 0.04503997 67.032967
## Chlorarachniophyceae 5.267654e-04 0.02251999 17.582418
## Chlorodendrophyceae 1.685649e-04 0.01125999 5.494505
## Cryptophyceae 2.170273e-03 0.06755996 26.373626
## Cyanobacteria 5.162067e+01 14.39027137 100.000000
## Dictyochophyceae 8.434567e-02 0.34905979 97.802198
## Dinophyceae 1.725683e-02 0.19141989 80.219780
## Eustigmatophyceae 7.775057e-03 0.06755996 61.538462
## Mamiellophyceae 2.629613e-02 0.18015989 37.362637
## Pelagophyceae 2.267198e-02 0.21393987 82.417582
## Prasinophyceae_clade-IX 3.761105e-02 0.25897984 87.912088
## Prasinophyceae_clade-VII 1.944818e-02 0.18015989 53.846154
## Prymnesiophyceae 5.653667e-01 3.78335773 100.000000
## Pyramimonadaceae 1.074601e-03 0.03377998 18.681319
## Rappemonads 2.865604e-03 0.07881995 45.054945
## Trebouxiophyceae 4.214123e-05 0.01125999 1.098901
## other_Prasinophyceae 5.689066e-04 0.02251999 17.582418
## other_bacteria 4.722683e+01 78.02049319 100.000000
## other_plastids 3.491190e-01 1.91419885 100.000000
Reads per class vs. OTUs per class:
Reads per class vs. samples in which they occurr:
PHOTOTROPHS
Absolute values
## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 450 14 42
## Bolidophyceae 271 4 61
## Chlorarachniophyceae 25 2 16
## Chlorodendrophyceae 8 1 5
## Cryptophyceae 103 6 24
## Cyanobacteria 2449889 1278 91
## Dictyochophyceae 4003 31 89
## Dinophyceae 819 17 73
## Eustigmatophyceae 369 6 56
## Mamiellophyceae 1248 16 34
## Pelagophyceae 1076 19 75
## Prasinophyceae_clade-IX 1785 23 80
## Prasinophyceae_clade-VII 923 16 49
## Prymnesiophyceae 26832 336 91
## Pyramimonadaceae 51 3 17
## Rappemonads 136 7 41
## Trebouxiophyceae 2 1 1
## other_Prasinophyceae 27 2 16
## other_plastids 16569 170 91
Relative values
## reads_per_class OTUs_per_class samples_per_class
## 100.000 100.000 1046.154## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 1.796704e-02 0.71721311 46.153846
## Bolidophyceae 1.082015e-02 0.20491803 67.032967
## Chlorarachniophyceae 9.981690e-04 0.10245902 17.582418
## Chlorodendrophyceae 3.194141e-04 0.05122951 5.494505
## Cryptophyceae 4.112456e-03 0.30737705 26.373626
## Cyanobacteria 9.781613e+01 65.47131148 100.000000
## Dictyochophyceae 1.598268e-01 1.58811475 97.802198
## Dinophyceae 3.270002e-02 0.87090164 80.219780
## Eustigmatophyceae 1.473297e-02 0.30737705 61.538462
## Mamiellophyceae 4.982859e-02 0.81967213 37.362637
## Pelagophyceae 4.296119e-02 0.97336066 82.417582
## Prasinophyceae_clade-IX 7.126926e-02 1.17827869 87.912088
## Prasinophyceae_clade-VII 3.685240e-02 0.81967213 53.846154
## Prymnesiophyceae 1.071315e+00 17.21311475 100.000000
## Pyramimonadaceae 2.036265e-03 0.15368852 18.681319
## Rappemonads 5.430039e-03 0.35860656 45.054945
## Trebouxiophyceae 7.985352e-05 0.05122951 1.098901
## other_Prasinophyceae 1.078022e-03 0.10245902 17.582418
## other_plastids 6.615465e-01 8.70901639 100.000000
Reads per class vs. OTUs per class:
Reads per class vs. samples in which they occurr:
Absolute values of cyanobacteria groups richness and abundance:
## reads_per_class OTUs_per_class
## Prochlorococcus 2287847 1036
## Synechococcus 152047 167
## other_cyanobacteria 9995 75Relative values of Cyanobacteria groups richness and abundance:
## reads_per_class OTUs_per_class
## Prochlorococcus 93.3857411 81.064163
## Synechococcus 6.2062812 13.067293
## Other cyanobacteria 0.4079777 5.868545
PROTISTS
## [1] 674## [1] 54697Absolute values
## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 450 14 42
## Bolidophyceae 271 4 61
## Chlorarachniophyceae 25 2 16
## Chlorodendrophyceae 8 1 5
## Cryptophyceae 103 6 24
## Dictyochophyceae 4003 31 89
## Dinophyceae 819 17 73
## Eustigmatophyceae 369 6 56
## Mamiellophyceae 1248 16 34
## Pelagophyceae 1076 19 75
## Prasinophyceae_clade-IX 1785 23 80
## Prasinophyceae_clade-VII 923 16 49
## Prymnesiophyceae 26832 336 91
## Pyramimonadaceae 51 3 17
## Rappemonads 136 7 41
## Trebouxiophyceae 2 1 1
## other_Prasinophyceae 27 2 16
## other_plastids 16569 170 91
Relative values
## reads_per_class OTUs_per_class samples_per_class
## 100.0000 100.0000 946.1538## reads_per_class OTUs_per_class samples_per_class
## Bacillariophyceae 0.822714226 2.0771513 46.153846
## Bolidophyceae 0.495456789 0.5934718 67.032967
## Chlorarachniophyceae 0.045706346 0.2967359 17.582418
## Chlorodendrophyceae 0.014626031 0.1483680 5.494505
## Cryptophyceae 0.188310145 0.8902077 26.373626
## Dictyochophyceae 7.318500101 4.5994065 97.802198
## Dinophyceae 1.497339891 2.5222552 80.219780
## Eustigmatophyceae 0.674625665 0.8902077 61.538462
## Mamiellophyceae 2.281660786 2.3738872 37.362637
## Pelagophyceae 1.967201126 2.8189911 82.417582
## Prasinophyceae_clade-IX 3.263433095 3.4124629 87.912088
## Prasinophyceae_clade-VII 1.687478289 2.3738872 53.846154
## Prymnesiophyceae 49.055706894 49.8516320 100.000000
## Pyramimonadaceae 0.093240946 0.4451039 18.681319
## Rappemonads 0.248642522 1.0385757 45.054945
## Trebouxiophyceae 0.003656508 0.1483680 1.098901
## other_Prasinophyceae 0.049362854 0.2967359 17.582418
## other_plastids 30.292337788 25.2225519 100.000000
Reads per class vs. OTUs per class:
Reads per class vs. samples in which they occurr:
